Vegetation change of the Arctic tundra due to global warming is a well-known process, but the implication for the belowground microbial communities, key in nutrient cycling and decomposition, is poorly understood. We characterized the fungal and bacterial abundances in litter and soil layers across 16 warming experimental sites at 12 circumpolar locations. We investigated the relationship between microbial abundances and nitrogen (N) and carbon (C) isotopic signatures, indicating shifts in microbial processes with warming. Microbial abundances were 2–3 orders of magnitude larger in litter than in soil. Local, site-dependent responses of microbial abundances were variable, and no general effect of warming was detected. The only generalizable trend across sites was a dependence between the warming response ratios and C:N ratio in controls, highlighting a legacy of the vegetation on the microbial response to warming. We detected a positive effect of warming on the litter mass and δ15N, which was linked to bacterial abundance under warmed conditions. This effect was stronger in experimental sites dominated by deciduous shrubs, suggesting an altered bacterial N-cycling with increased temperatures, mediated by the vegetation, and with possible consequences on ecosystem feedbacks to climate change.